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Forum: Metagenomics 08-24-2017, 04:36 AM
Replies: 0
Views: 529
Posted By nouse
Normalization for NGS count data with high variance between observations / uneven com

Dear community,

we have a MiSeq 16S-dataset featuring samples from enrichment studies, i.e. communities from a time series in which some OTUs become dominant over time, e.g. up to 90% of all...
Forum: Illumina/Solexa 02-15-2017, 01:04 AM
Replies: 5
Views: 808
Posted By nouse
Thanks for your answer. From my experience...

Thanks for your answer.
From my experience with the HiSeq, the raw sequences i got included barcodes and pcr primers (which makes sense, since they have been sequenced after all).

This indicates...
Forum: Illumina/Solexa 02-14-2017, 02:21 PM
Replies: 5
Views: 808
Posted By nouse
What is the official "first sequenced position" (for overlap calculation)??

The question ermerged after reviewing this older application note by Illumina:

https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/appnote_miseq_16S.pdf

Their...
Forum: Sample Prep / Library Generation 02-14-2017, 06:46 AM
Replies: 0
Views: 410
Posted By nouse
batch tool for checking primers

Hi, i am about to order 400 barcoded primers (100 barcodes + 2 directions x 2 Genes of Interest).

Usually i check my primers with the OligoAnalyzer by IDT, but they dont accept the upload of fasta...
Forum: Illumina/Solexa 01-15-2015, 03:40 AM
Replies: 2
Views: 1,232
Posted By nouse
Number of clusters are way too high in my QIIME analysis

Hi there,

I am using QIIME to process my dataset of 2 million joined MiSeq PE-reads (~500 bp) from a 16S rDNA community survey.

I do have the output of the proprietory pipeline of the...
Forum: Illumina/Solexa 01-15-2015, 03:28 AM
Replies: 0
Views: 616
Posted By nouse
Manipulating the quality file during fasta-demultiplexing with QIIME

Hi!

I am using QIIME to process my dataset of 2 million joined PE-reads (~500 bp).

I want to use cd-hit as my OTU picker. cd-hit requires a fastq file with every sequence startsing with the...
Forum: Illumina/Solexa 12-18-2014, 09:04 AM
Replies: 3
Views: 1,044
Posted By nouse
oh, i just saw the description of trimmomatic. ...

oh, i just saw the description of trimmomatic.
Could you please advice me to remove adapters + 8mer barcodes from the unpaired r1 r2 fastq files? I would be very happy!
Forum: Illumina/Solexa 12-18-2014, 04:36 AM
Replies: 3
Views: 1,044
Posted By nouse
Removal of adapters and barcodes

Hi!

I want to compare an existing result from QIIME to cd-hit-otu-illumina.


cd-hit asks

"Barcodes should be removed. All the tags must start at 5' with the same rRNA primer shared by all...
Forum: Bioinformatics 01-28-2014, 07:34 AM
Replies: 364
Views: 151,634
Posted By nouse
Thanks for the quick answer. My 460 million...

Thanks for the quick answer.

My 460 million reads were processed over night without troubles. I was just impatient.

I have paired end data, and it seems like some of the samples have...
Forum: Bioinformatics 01-27-2014, 08:06 AM
Replies: 364
Views: 151,634
Posted By nouse
Hi there! Three quick questions.... 1....

Hi there!

Three quick questions....
1. What is the maximum amount of data fastqc can handle?
I am trying to analyze a huge concatenated sample of illumina data, but its stuck @"Starting...
Forum: Bioinformatics 09-16-2013, 05:44 AM
Replies: 2
Views: 6,695
Posted By nouse
Renaming of Fasta headers according to their container name

Hi there,
i am a somewhat beginner in bioinformatics, so please apologize if i am asking any silly questions.

I do have several dozens of files containing millions of processed illumina reads....
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